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mascaretti
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@mascaretti-22851
Last seen 4.8 years ago
Installation of Rgraphviz fails
Installation of the Rgrapvhiz package fails.
Installation code
To install the package, I run the following:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Rgraphviz")
Error
The installation process exits with non-zero status reporting the following:
Error: package or namespace load failed for ‘Rgraphviz’:
.onLoad failed in loadNamespace() for 'Rgraphviz', details:
call: value[[3L]](cond)
error: unable to load shared object '/home/andrea/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rgraphviz/00new/Rgraphviz/libs/Rgraphviz.so':
/home/andrea/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-Rgraphviz/00new/Rgraphviz/libs/Rgraphviz.so: undefined symbol: _ZGVdN4vv___pow_finite
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Rgraphviz is unable to be loaded. This typically is a symptom of an
installation problem. From 2.x.x onwards, Graphviz ought to come
bundled with Rgraphviz.
If you are trying to use an external Graphviz, see additional
instructions in the 'README' file of the Rgraphviz 'source'
distribution, available at
http://bioconductor.org/packages/release/bioc/html/Rgraphviz.html
Ask further questions on the Bioconductor mailing list
http://bioconductor.org/docs/mailList.html
Errore: loading failed
Esecuzione interrotta
Session Info
The output of sessionInfo()
is the following:
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblas_zenp-r0.3.7.so
locale:
[1] LC_CTYPE=it_IT.UTF-8 LC_NUMERIC=C LC_TIME=it_IT.UTF-8 LC_COLLATE=it_IT.UTF-8 LC_MONETARY=it_IT.UTF-8
[6] LC_MESSAGES=it_IT.UTF-8 LC_PAPER=it_IT.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.10 compiler_3.6.2 htmltools_0.4.0 tools_3.6.2 yaml_2.2.1 Rcpp_1.0.3 rmarkdown_2.1
[8] knitr_1.27 xfun_0.12 digest_0.6.23 rlang_0.4.4 evaluate_0.14
GCC Version
I am running GCC 9.2.0
~ » gcc -v andrea@andrea-pc
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/lib/gcc/x86_64-pc-linux-gnu/9.2.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: /build/gcc/src/gcc/configure --prefix=/usr --libdir=/usr/lib --libexecdir=/usr/lib --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=https://bugs.archlinux.org/ --enable-languages=c,c++,ada,fortran,go,lto,objc,obj-c++,d --enable-shared --enable-threads=posix --with-system-zlib --with-isl --enable-__cxa_atexit --disable-libunwind-exceptions --enable-clocale=gnu --disable-libstdcxx-pch --disable-libssp --enable-gnu-unique-object --enable-linker-build-id --enable-lto --enable-plugin --enable-install-libiberty --with-linker-hash-style=gnu --enable-gnu-indirect-function --enable-multilib --disable-werror --enable-checking=release --enable-default-pie --enable-default-ssp --enable-cet=auto gdc_include_dir=/usr/include/dlang/gdc
Thread model: posix
gcc version 9.2.0 (GCC)
You were right. I should have included that I had a
Makevars
of the form:By changing the optimisation options, everything works alright. Many thanks!